You my friend, are a lifesaver!!! I have had my hardware & been working on & off on trying to get a good solid & stable build for about a year now (initially started under OSX 10.10.x). I did exactly as you instructed, including the BIOS settings. While there were a couple hiccups during the installation (some reboots that I wasn't expecting that sort of gave me a quick scare), my system is now up & running, and it appears to be working pretty well.
My biggest problem was the whole OsxAptioFixDrv drama. In previous attempts using other methods, I'd be OK with just the GPU, but the minute I added another card, things went to pieces. Tried all combinations of OsxAptioFixDrv2, plus the other options with Test2_2016, OsxAptioFix2Drv-free2000.efi, etc. etc. The system was very unstable & frequently would take me 3 or 4 attempts to boot up.
Note that I **did** have to add Test2-2016.efi to my build. Your instructions PLUS adding that is the magic formula for me in my case:
ASUS X99-DELUXE (1st gen)
i7 5930x
EVGA GTX 970
16GB Ripjaw
ThunderboltIIEX-Dual card
TB is working great - I have my OWC Thunderbolt 2 docking station hooked up to it, and listening to audio via the device's on-board USB audio (BTW, mobo onboard audio working ok with VooDooHDA kext). I've also connected a USB3 drive to the dock & works. I have a couple other TB devices that I will test further.
Things I still need to check/test: USB3 really runs at USB3 speed.
Wish list: a little overclocking to improve performance. I see a lot of folks with their X99 builds & successfully OC'ing to 4.3 GHz. When I had my build running (sort of) before under 10.10.x, the OC was working & I was getting some good GeekBench speeds. If anyone has any tips on how to take this build & do a little OC, I'm all ears.
Once again, MANY MANY thanks!!!
--B